Seed priming and abiotic stress tolerance in carrot: Unraveling the mechanisms of improved germination. by Marcin Nowicki, Marzena Nowakowska, Katarzyna Nowak, Wojciech Szczechura, Piotr Kaminski

“…Future research integrating omics approaches (e.g., transcriptomics, proteomics, metabolomics) will provide deeper insights into the molecular mechanisms that regulate stress tolerance, to aid in the development of more resilient carrot varieties suitable for cultivation under adverse environmental conditions.…”
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SUMOylation-regulated genes in colon cancer: expression patterns and clinical implications by Wen Peng, Zirong Yang, Ru Yan, Lan Mu, Lan Li, Shan Jin, Shisheng Tan

“…A comprehensive analysis of SUMOylation-regulated gene expression, clinical and prognostic value in CRC was performed using transcriptomic data from TCGA-COAD and GEO datasets. We identified 46 differentially expressed SUMOylation-regulated genes (33 upregulated, 13 downregulated) in CRC tumors versus normal tissues. …”
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PAQR6 as a prognostic biomarker and potential therapeutic target in kidney renal clear cell carcinoma by Tao Zou, Zongming Jia, Jixiang Wu, Xuxu Liu, Minghao Deng, Xuefeng Zhang, Yuxin Lin, Yuxin Lin, Jigen Ping

“…However, its biological function in kidney renal clear cell carcinoma (KIRC) and its potential as a therapeutic target remain underexplored.MethodsIn this study, PAQR6 was identified as a critical oncogene by WGCNA algorithm and differential gene expression analysis using TCGA - KIRC and GSE15641 data. The differences in PAQR6 expression and its association with KIRC survival outcomes were investigated, and transcriptomic data were used to further elucidate PAQR6’s biological functions. …”
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Multi-omics reveals the mechanism of quality discrepancy between Gayal (Bos frontalis) and yellow cattle beef by Lin Han, Runqi Fu, Chunjia Jin, Huan Gao, Binlong Fu, Qian Li, Ye Yu, Min Qi, Jiawei Zhang, Shengyong Mao, Jing Leng

“…Results The results demonstrated that Gayal cattle exhibited superior meat quality, characterized by higher levels of protein, flavor-enhancing and essential amino acids, total amino acids, and polyunsaturated fatty acids (PUFAs), alongside reduced fat content, with similar trends observed in serum hormone and amino acid profiles. Distinct differences in gut microbial composition, enzymatic activities, and metabolites were observed between the breeds. …”
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Focusing on DC cells to optimize the prediction of prognosis and innovative treatment strategies for colon cancer by Chaobo Chen, Zhengqiu Wang, Bo Xi, Zipeng Xu, Chunlong Zhao, Weidong Hu, Chen Ge, Genxi Tong, Fengjun Cai, Mingli Zhou, Yihang Yuan

“…The DCRI effectively stratified patients into high- and low-DCRI groups, with significant survival differences. High-DCRI patients exhibited distinct immune infiltration patterns, higher MSI scores, and increased sensitivity to immunotherapy. …”
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An interpretable survival model for diffuse large B-cell lymphoma patients using a biologically informed visible neural network by Jie Tan, Jiancong Xie, Jiarong Huang, Weizhen Deng, Hua Chai, Yuedong Yang

“…However, existing DLBCL prognostic models are mainly based on transcriptomic profiles, while genetic variation detection is more commonly used in clinical practice. …”
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Precision prognostication in neuroblastomas via clinically validated E2F activity signatures by Donghan Cai, Donghan Cai, Huihuang Xu, Huihuang Xu, Shiwei He, Di Xu, Di Xu, Lizhi Li, Lizhi Li

“…E2F transcription factors (E2Fs) are pivotal regulators of cell cycle progression and immune modulation, yet their prognostic and therapeutic implications in NB remain underexplored.MethodsUsing transcriptomic data from the GEO, TARGET, and E-MTAB-8248 cohorts, we identified E2F-associated molecular subtypes via consensus clustering. …”
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Cellular imbalance in proximal and distal lung of CFTR −/− sheep in utero and at birth by Shih-Hsing Leir, Svyatoslav Tkachenko, Alekh Paranjapye, Arnaud J. Van Wettere, Jenny L. Kerschner, Iuri Viotti Perisse, Cheyenne M. Marriott, Tayler Patrick, Ying Liu, Kenneth L. White, Irina A. Polejaeva, Ann Harris

“…Methods Here we used the sheep model of CF (CFTR −/− ) and age-matched wild-type (WT) sheep of the same breed to investigate the single cell transcriptomes of proximal and distal lung tissue at 80 days and 120 days of gestation and at term (147 days). …”
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Genome-wide association study identifies candidate SNP markers and genes associated with low nitrogen tolerance in Brassica napus by Jingdong Chen, Jingdong Chen, Lingli Xie, Xianfei Hou, Rui Yang, Jin Liu, Xigang Dai, Tianyuan Xue, Shuai Yin, Benbo Xu, Xuekun Zhang, Changli Zeng, Jinsong Xu

“…Comparative analysis with previous studies revealed unique SNP loci, likely due to differences in germplasm, nitrogen levels, and experimental design. …”
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Prototol for the Prospective Sample Collection for Cancer of Bladder (ProCaB) Trial by the Cancer of the Bladder Leuven (CaBLe) Consortium by Murat Akand, Tim Muilwijk, Ben Van Cleynenbreugel, Thomas Gevaert, Steven Joniau, Frank Van der Aa

“…Multiomics (genomics, epigenetics, transcriptomics, proteomics, lipidomics, metabolomics) and immunohistopathology analyses will be performed on appropriate samples. …”
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Integrated single cell and bulk RNA sequencing analyses reveal the impact of tryptophan metabolism on prognosis and immunotherapy in colon cancer by Yanyan Hu, Ximo Xu, Hao Zhong, Chengshen Ding, Sen zhang, Wei Qin, Enkui Zhang, Duohuo Shu, Mengqin Yu, Naijipu Abuduaini, Xiao Yang, Bo Feng, Jianwen Li

“…Two distinct subtypes of colon cancer patients emerged, exhibiting significant prognostic and immune cell infiltration differences. The high-risk group demonstrated a poorer prognosis (p < 0.001), advanced clinical stage (p < 0.001), and elevated immunosuppressive cell expression (p < 0.05). …”
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Selenium nanoparticles induce differential shoot/root response of Capsicum annuum seedlings revealed by non-targeted metabolomic analysis by Tonatiu Campos-García, María Fernanda Hernández-Soltero, Overlin Brandon Hernández-Fernández, Juan Vázquez-Martínez, Soledad García-Morales

“…Nevertheless, a multi-omics approach combining targeted transcriptomic and metabolomic analyses is needed to fully elucidate the mechanisms underlying the SeNPs effect on plant response to environmental stressors.…”
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Loss of CTRP10 results in female obesity with preserved metabolic health by Fangluo Chen, Dylan C Sarver, Muzna Saqib, Leandro M Velez, Susan Aja, Marcus M Seldin, G William Wong

“…Obesity is largely uncoupled from metabolic dysregulation in female KO mice. Multi-tissue transcriptomic analyses highlighted gene expression changes and pathways associated with insulin-sensitive obesity. …”
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Cellular hierarchy framework based on single-cell/multi-patient sample sequencing reveals metabolic biomarker PYGL as a therapeutic target for HNSCC by Jiezhong Guan, Xi Xu, Guo Qiu, Chong He, Xiaoyue Lu, Kang Wang, Xinyu Liu, Yuanyuan Li, Zihang Ling, Xuan Tang, Yujie Liang, Xiaoan Tao, Bin Cheng, Bo Yang

“…Subsequent analysis targeted for phenotype differences between the METArisk subgroups identified PYGL as a key metabolism-related biomarker that enhances malignancy and chemotherapy resistance by GSH/ROS/p53 pathway, leading to poor prognosis of HNSCC. …”
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Investigation of transcriptional and immunological disparities among patient groups with varied prognostic risk factors in cholangiocarcinoma by Baoluhe Zhang, Bao Jin, Xiang'an Wu, Jiali Xing, Xiao Liu, Xueshuai Wan, Haifeng Xu, Yiyao Xu, Yilei Mao, Qian Chen, Yating Bai, Mei Guan, Shunda Du

“…Methods and Results The transcriptomic and whole‐exome sequencing data obtained from paired tissues of 70 were analyzed, grouping them based on progression‐free survival (PFS), differentiation degree, and lymph node metastasis. …”
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Multi-omics integration reveals immune hallmarks and biomarkers associated with FLT3 inhibitor sensitivity in FLT3-mutated AML by Mingming Niu, Ning Wang, Dandan Yang, Lixia Fu, Yang Yang, Long Shen, Hong Wang, Xianfeng Shao

“…Our analysis revealed significant differences in RNA and protein expression profiles between FLT3-mutant and wild-type AML cases, with a particularly striking association between FLT3 mutations and immune suppression. …”
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Single-cell landscape of immunological responses in patients with juvenile idiopathic arthritis by Yun Liu, Xiwen Luo, Liuqing Yang, Qiang Luo, Xiya Luo, Li Xu, Yating Wang, Yunfei An, Yupeng Cun, Xuemei Tang

“…The study aimed to analyze the single-cell transcriptomes of immune cells in juvenile idiopathic arthritis (JIA) patients to understand the cellular heterogeneity within the immune system. …”
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Inflammatory markers after supplementation with marine n-3 or plant n-6 PUFAs: A randomized double-blind crossover study by Elise Grytten, Johnny Laupsa-Borge, Kaya Cetin, Pavol Bohov, Jan Erik Nordrehaug, Jon Skorve, Rolf K. Berge, Elin Strand, Bodil Bjørndal, Ottar K. Nygård, Espen Rostrup, Gunnar Mellgren, Simon N. Dankel

“…Adipose transcriptomics revealed overall downregulation of genes related to inflammatory processes after n-3 and upregulation after n-6, partly correlating with changes in circulatory markers. …”
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Immune Characters and Plasticity of the Sentinel Lymph Node in Colorectal Cancer Patients by Xiaoyun Li, Jingling Tang, Hang Du, Xinjun Wang, Liyun Wu, Pingsheng Hu, Hua Zhang, Ruyi Zhang, Yuan Yang

“…Differential expression and distribution of characteristic immune cell markers were analyzed by multiplex immunohistochemistry (mIHC). Transcriptomics analysis was conducted to compare the differences in the expression of immune-related genes among lymph nodes. …”
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Behçet syndrome: The disturbed balance between anti‐ (CLEC12A, CLC) and proinflammatory (IFI27) gene expressions by Ali Kemal Oğuz, Çağdaş Şahap Oygür, Seda Taşır, Hilal Özdağ, Mehmet Nejat Akar

“…A microarray‐based comparative transcriptomic analysis was performed to elucidate the molecular mechanisms of BS and identify any potential therapeutic targets. …”
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